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Rewards and dangers of regulatory innovation. 监管创新的回报与危险。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-20 DOI: 10.1016/j.tig.2024.07.010
Luca Comai
{"title":"Rewards and dangers of regulatory innovation.","authors":"Luca Comai","doi":"10.1016/j.tig.2024.07.010","DOIUrl":"10.1016/j.tig.2024.07.010","url":null,"abstract":"<p><p>Adaptive evolution often involves structural variation affecting genes or cis-regulatory changes that engender novel and favorable gain-of-function gene regulation. Such mutation could result in a favorable dominant trait. At the same time, the gene product could be dosage sensitive if its change in concentration disrupts another trait. As a result, the mutant allele would display dosage-sensitive pleiotropy (DSP). By minimizing imbalance while conserving the favorable dominant effect, heterozygosity can increase fitness and result in heterosis. The properties of these alleles are consistent with evidence from multiple studies that indicate increased fitness of heterozygous regulatory mutations. DSP can help explain mysterious properties of heterosis as well as other effects of hybridization.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"917-926"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Wheat genomics: genomes, pangenomes, and beyond. 小麦基因组学：基因组、泛基因组及其他。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-26 DOI: 10.1016/j.tig.2024.07.004
Vijay K Tiwari, Gautam Saripalli, Parva K Sharma, Jesse Poland
{"title":"Wheat genomics: genomes, pangenomes, and beyond.","authors":"Vijay K Tiwari, Gautam Saripalli, Parva K Sharma, Jesse Poland","doi":"10.1016/j.tig.2024.07.004","DOIUrl":"10.1016/j.tig.2024.07.004","url":null,"abstract":"<p><p>There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"982-992"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder. ReNU综合症--一种新发现的神经发育障碍。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-10-01 DOI: 10.1016/j.tig.2024.09.005
Vanessa F Burns, Elizabeth J Radford
{"title":"ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder.","authors":"Vanessa F Burns, Elizabeth J Radford","doi":"10.1016/j.tig.2024.09.005","DOIUrl":"10.1016/j.tig.2024.09.005","url":null,"abstract":"<p><p>Two recent papers have identified genetic variants in the noncoding gene RNU4-2 to cause a frequent neurodevelopmental disorder. This work will have a substantial impact on the rare disease community, leading to thousands of diagnoses worldwide. These studies also highlight the untapped diagnostic potential of noncoding regions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"914-916"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The very early evolution of biological complexity. 生物复杂性的早期进化
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-09-25 DOI: 10.1016/j.tig.2024.09.001
Aaron D Goldman, Gregory P Fournier
{"title":"The very early evolution of biological complexity.","authors":"Aaron D Goldman, Gregory P Fournier","doi":"10.1016/j.tig.2024.09.001","DOIUrl":"10.1016/j.tig.2024.09.001","url":null,"abstract":"<p><p>All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"912-913"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational methods for allele-specific expression in single cells. 单细胞中等位基因特异性表达的计算方法。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-10 DOI: 10.1016/j.tig.2024.07.003
Guanghao Qi, Alexis Battle
{"title":"Computational methods for allele-specific expression in single cells.","authors":"Guanghao Qi, Alexis Battle","doi":"10.1016/j.tig.2024.07.003","DOIUrl":"10.1016/j.tig.2024.07.003","url":null,"abstract":"<p><p>Allele-specific expression (ASE) is a powerful signal that can be used to investigate multiple molecular mechanisms, such as cis-regulatory effects and imprinting. Single-cell RNA-sequencing (scRNA-seq) enables ASE characterization at the resolution of individual cells. In this review, we highlight the computational methods for processing and analyzing single-cell ASE data. We first describe a bioinformatics pipeline to obtain ASE counts from raw reads synthesized from previous literature. We then discuss statistical methods for detecting allelic imbalance and its variability across conditions using scRNA-seq data. In addition, we describe other methods that use single-cell ASE to address specific biological questions. Finally, we discuss future directions and emphasize the need for an integrated, optimized bioinformatics pipeline, and further development of statistical methods for different technologies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"939-949"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Honeybees' novel complementary sex-determining system: function and origin. 蜜蜂的新型互补性决定系统：功能和起源。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-09-03 DOI: 10.1016/j.tig.2024.08.001
Jana Seiler, Martin Beye
{"title":"Honeybees' novel complementary sex-determining system: function and origin.","authors":"Jana Seiler, Martin Beye","doi":"10.1016/j.tig.2024.08.001","DOIUrl":"10.1016/j.tig.2024.08.001","url":null,"abstract":"<p><p>Complementary sex determination regulates female and male development in honeybees (Apis mellifera) via heterozygous versus homo-/hemizygous genotypes of the csd (complementary sex determiner) gene involving numerous naturally occurring alleles. This lineage-specific function offers a rare opportunity to understand an undescribed regulatory mechanism and the molecular evolutionary path leading to this mechanism. We reviewed recent advances in understanding how Csd recognizes different versus identical protein variants, how these variants regulate downstream pathways and sexual differentiation, and how this mechanism has evolved and been shaped by evolutionary forces. Finally, we highlighted the shared regulatory principles of sex determination despite the diversity of primary signals and demonstrated that lineage-specific mutations are very informative for characterizing newly evolved functions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"969-981"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries. 减数分裂过程中同源染色体间的交叉重组：最新进展与未解之谜。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-25 DOI: 10.1016/j.tig.2024.09.009
Lisette Payero, Eric Alani
{"title":"Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries.","authors":"Lisette Payero, Eric Alani","doi":"10.1016/j.tig.2024.09.009","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.009","url":null,"abstract":"<p><p>Crossing over between homologous chromosomes in meiosis is essential in most eukaryotes to produce gametes with the correct ploidy. Meiotic crossovers are typically evenly spaced, with each homolog pair receiving at least one crossover. The association of crossovers with distal sister chromatid cohesion is critical for the proper segregation of homologs in the first meiotic division. Studies in baker's yeast (Saccharomyces cerevisiae) have shown that meiotic crossovers result primarily from the biased resolution of double Holliday junction (dHJ) recombination intermediates through the actions of factors that belong to the DNA mismatch repair family. These findings and studies involving fine-scale mapping of meiotic crossover events have led to a new generation of mechanistic models for crossing over that are currently being tested.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Disentangling variational bias: the roles of development, mutation, and selection. 分解变异偏差：发育、变异和选择的作用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-22 DOI: 10.1016/j.tig.2024.09.008
Haoran Cai, Diogo Melo, David L Des Marais
{"title":"Disentangling variational bias: the roles of development, mutation, and selection.","authors":"Haoran Cai, Diogo Melo, David L Des Marais","doi":"10.1016/j.tig.2024.09.008","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.008","url":null,"abstract":"<p><p>The extraordinary diversity and adaptive fit of organisms to their environment depends fundamentally on the availability of variation. While most population genetic frameworks assume that random mutations produce isotropic phenotypic variation, the distribution of variation available to natural selection is more restricted, as the distribution of phenotypic variation is affected by a range of factors in developmental systems. Here, we revisit the concept of developmental bias - the observation that the generation of phenotypic variation is biased due to the structure, character, composition, or dynamics of the developmental system - and argue that a more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map will produce fundamental insights into evolutionary processes, with potentially important consequences on the relation between micro- and macro-evolution. We discuss the hierarchical relationships between different types of variational biases, including mutation bias and developmental bias, and their roles in shaping the realized phenotypic space. Furthermore, we highlight the challenges in studying variational bias and propose potential approaches to identify developmental bias using modern tools.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unraveling aging from transcriptomics. 从转录组学揭示衰老。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-17 DOI: 10.1016/j.tig.2024.09.006
Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han
{"title":"Unraveling aging from transcriptomics.","authors":"Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han","doi":"10.1016/j.tig.2024.09.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.006","url":null,"abstract":"<p><p>Research into aging constitutes a pivotal endeavor aimed at elucidating the underlying biological mechanisms governing aging and age-associated diseases, as well as promoting healthy longevity. Recent advances in transcriptomic technologies, such as bulk RNA sequencing (RNA-seq), single-cell transcriptomics, and spatial transcriptomics, have revolutionized our ability to study aging at unprecedented resolution and scale. These technologies present novel opportunities for the discovery of biomarkers, elucidation of molecular pathways, and development of targeted therapeutic strategies for age-related disorders. This review surveys recent breakthroughs in different types of transcripts on aging, such as mRNA, long noncoding (lnc)RNA, tRNA, and miRNA, highlighting key findings and discussing their potential implications for future studies in this field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A bioinformatics toolbox to prioritize causal genetic variants in candidate regions. 生物信息学工具箱，用于确定候选区域因果遗传变异的优先次序。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-15 DOI: 10.1016/j.tig.2024.09.007
Martin Šimon, Maša Čater, Tanja Kunej, Nicholas M Morton, Simon Horvat
{"title":"A bioinformatics toolbox to prioritize causal genetic variants in candidate regions.","authors":"Martin Šimon, Maša Čater, Tanja Kunej, Nicholas M Morton, Simon Horvat","doi":"10.1016/j.tig.2024.09.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.007","url":null,"abstract":"<p><p>This review addresses the significant challenge of identifying causal genetic variants within quantitative trait loci (QTLs) for complex traits and diseases. Despite progress in detecting the ever-larger number of such loci, establishing causality remains daunting. We advocate for integrating bioinformatics and multiomics analyses to streamline the prioritization of candidate genes' variants. Our case study on the Pla2g4e gene, identified previously as a positional candidate obesity gene through genetic mapping and expression studies, demonstrates how applying multiomic data filtered through regulatory elements containing SNPs can refine the search for causative variants. This approach can yield results that guide more efficient experimental strategies, accelerating genetic research toward functional validation and therapeutic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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